The Camelid Genome Variation Database : An Integrative Database for Studying Camelid Genetic Evolution , Biological Characteristics and Desert Adaption

The Camelid Genome Variation Database: An Integrative Database for Studying Camelid Genetic Evolution, Biological Characteristics and Desert Adaption Tuya Saren, Haiqing Liu and Rimutu Ji, (1)Inner Mongolia Institute of Camel Research, Alxa, Inner Mongolia, China, (2)Inner Mongolia Agricultural University, Huhhot, China Aims: The camelids including Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedaries) and alpaca (Vicugna pacos), are important economically livestock for transportation and production (meat, milk and wool). During the long-term natural selection, they have acquired many unique abilities to adapt to the desert environment. In recent decades, their genetic diversity, evolutionary history and biological characteristics have been elucidated by independent studies. However, these studies of camelids were scattered and the amount of available data were still limited. Our database Camel GVD is designed to provide comprehensive resources for camelid genome studies. Methods: Camel GVD is a web-based large-scale whole genome variation database, including single nucleotide polymorphisms (SNPs), insertions and deletions (Indels). Results: It contains a collection of ~19 million variants identified by whole-genome sequencing of over 100 camels from our original research. It also contains all the public available camelid genome data. Camel GVD integrates a comprehensive collection of variation related information, including variation annotations, associated genes/proteins/transcripts, sample locations, population introductions, and allele frequencies. It offers several functions, for users to search, display and retrieve the variations and their annotations. Camel GVD also provides several data browsing functionalities under the “Browse” pull-down menu, including variant alignment, coverage and genome feature files. Users can select one sample or several samples to browse the information. It also provides a special function to display gene information of several camel features based on the existing studies to provide convenience for users. In addition, the vcf files can be downloaded for advanced data mining and analysis. Thus, Camel GVD is expected to become a bioinformatics platform for studying the evolution, genetic breeding, biological characteristics and functional genes of camelids. Conclusion: Our database Camel GVD is the first large-scale, and so far the most comprehensive collection of genomic variant data from over 100 individual camelids. Compared with one similar database, our database provides both SNPs and Indels information, and also provides functional gene information associated with camel genetic and biological characteristics. This database is helpful to facilitate the future studies of population genetics and molecular biology in camelids.